Digital Commons Network^™

A Phylogenomic Supertree Of Birds, R T. Kimball, C H. Oliveros, N Wang, N D. White, R T. Kimball, D J. Field, D T. Ksepka, R T. Chesser, R G. Moyle, M J. Braun, R T. Brumfield, B C. Faircloth, B T. Smith, E L. Braun

Faculty Publications

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap …

Resetting The Table For People And Plants: Botanic Gardens And Research Organizations Collaborate To Address Food And Agricultural Plant Blindness, Sarada Krishnan, Tara Moreau, Jeff Kuehny, Ari Novy, Stephanie L. Greene, Colin K. Khoury

Faculty Publications

Societal Impact Statement: Food and agricultural plants are integral to human well-being. Due to their universal importance, such plants would appear to represent an ideal entryway by which to address plant blindness. However, with limited opportunities for direct contact with agriculture, many people cannot appreciate the flora that feed us every day. We provide examples of informal education initiatives aimed at increasing public awareness and appreciation of food and agricultural plants, made possible through collaborations between botanic gardens, academic institutions, nonprofits, and agricultural research organizations. We hope these examples encourage and inspire organizations to further utilize food and agricultural plants …

Elemental Composition, Phosphorous Uptake, And Characteristics Of Growth Of A Sar11 Strain In Batch And Continuous Culture, Scott R. Grant, Matthew J. Church, Sara Ferrón, Edward A. Laws, Michael S. Rappé

Faculty Publications

In this study, a strain of SAR11 subgroup IIIa (termed HIMB114) was grown in seawater-based batch and continuous culture in order to quantify cellular features and metabolism relevant to SAR11 ecology. We report some of the first direct measurements of cellular elemental quotas for nitrogen (N) and phosphorus (P) for SAR11, grown in batch culture: 1.4 0.9 fg N and 0.44 0.01 fg P, respectively, that were consistent with the small size of HIMB114 cells (average volume of 0.09 m³). However, the mean carbon (C) cellular quota of 50 47 fg C was anomalously high, but variable. The …

Hole Filling In 3d Scans For Digital Anthropometric Applications, Sima Sobhiyeh, Marcelline Dechenaud, Alexander Dunkel, Margarite Laborde, Samantha Kennedy, John Shepherd, Steven Heymsfield, Peter Wolenski

Faculty Publications

Anthropometric measurements have been used to assess an individual's body composition, disease risk, and nutritional status. Three-dimensional (3D) optical devices can rapidly acquire body surface scans in the form of a triangular mesh which can then be used to obtain anthropometric measurements such as body volume, limb lengths, and circumferences; however, the meshes provided by some scanners may include missing data patches known as holes. These need to be repaired in order to obtain correct landmark detection and automatic calculation of anthropometric measurements -especially body volume. In this study, we present ScReAM (Scan Reconstruction for Anthropometric Measurements) which is a …

Genome Sequence Of The Radiation-Resistant Bacterium Deinococcus Radiophilus Atcc 27603, Claudia R. Maynard, Kyle S. Maclea

Faculty Publications

The pigmented bacterium Deinococcus radiophilus, which is highly resistant to radiation exposure, was first isolated from irradiated lizardfish. We report a genome assembly of D. radiophilus UWO 1055T (=ATCC 27603T), with a predicted genome size of 2.7 Mbp (62.66% G+C content). A number of CRISPR-associated proteins and two CRISPR arrays were identified.

Preliminary Investigation Of A Diverse Megafossil Floral Assemblage From The Middle Miocene Of Southern Mississippi, Usa, Daniel M. Mcnair, Debra Z. Stults, Brian Axsmith, Mac H. Alford, James E. Starnes

Faculty Publications

Our understanding of Miocene floras in eastern North America is hampered by the rarity of megafossil sites. An early report from the middle Miocene Hattiesburg Formation in Mississippi included palms and Ulmus. A later report listed Taxodium, Salix, either Morus or Celtis, and monocot fragments. The floral assemblage described here was recently recovered from along the Bouie River in southern Mississippi. Ferns are represented by complete Salvinia specimens including attached sporocarps, Woodwardia, and Osmunda. Conifers are represented by branchlets of Taxodium. Angiosperms include leaves attributable to the Lauraceae. Platanus is known from leaves, stipules, and fruits. …

Scale Dependence Of Sex-Specific Movement In A Small-Bodied Stream Fish, Scott R. Clark, Brian R. Kreiser, Jacob F. Schraefer, Laura K. Stewart

Faculty Publications

1. Animal movement at localised scales is often modulated by competing pressures such as avoiding predators while acquiring resources and mates. The relative magnitude of these trade‐offs may affect males and females differently, often resulting in sex‐specific differences in movement.
2. Sex‐biases in movement have been linked to mating systems (e.g. monogamy or polygamy) in birds and mammals; however, this relationship has received less attention among fishes. Using passive integrated transponder tags and a series of stationary antennas, we evaluated the movement dynamics of a small‐bodied, sexually dimorphic stream fish Fundulus olivaceus over a 30‐day period in a fourth‐order tributary to the …

The Molecular Biogeography Of The Indo-Pacific: Testing Hypotheses With Multispecies Genetic Patterns, Eric D. Crandall, Cynthia Riginos, Chris E. Bird, Libby Liggins, Eric Treml, Maria Beger, Paul H. Barber, Sean R. Connolly, Peter F. Cowman, Joseph D. Dibattista, Jeff A. Eble, Sharon F. Magnuson, John B. Horne, Marc Kochzius, Harilaos A. Lessios, Shang Yin Vanson Liu, William B. Ludt, Hawis Madduppa, John M. Pandolfi, Robert J. Toonen, Michelle R. Gaither

Faculty Publications

Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test.

>Location: The Indo-Pacific Ocean.

Time Period: Pliocene through the Holocene.

Major Taxa Studied: Fifty-six marine species.

Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise Φ_ST, and these Φ_ST distributions were compared to distributions from randomized datasets and …

Why Nature Matters: Seventh-Day Adventist Education In The Anthropocene, Daniel Gonzalez-Socoloske

Faculty Publications

No abstract provided.

Observations And Modeling Of A Hydrothermal Plume In Yellowstone Lake, Robert A. Sohn, Karen Luttrell, Emily Shroyer, Christian Stranne, Robert N. Harris, Julia E. Favorito

Faculty Publications

©2019. American Geophysical Union. All Rights Reserved. Acoustic Doppler current profiler and conductivity-temperature-depth data acquired in Yellowstone Lake reveal the presence of a buoyant plume above the “Deep Hole” hydrothermal system, located southeast of Stevenson Island. Distributed venting in the ~200 × 200-m hydrothermal field creates a plume with vertical velocities of ~10 cm/s in the mid-water column. Salinity profiles indicate that during the period of strong summer stratification the plume rises to a neutral buoyancy horizon at ~45-m depth, corresponding to a ~70-m rise height, where it generates an anomaly of ~5% (−0.0014 psu) relative to background lake water. …

A Sustained Ocean Observing System In The Indian Ocean For Climate Related Scientific Knowledge And Societal Needs, J.C. Hermes, Y. Masumoto, L.M. Beal, M.K. Roxy, J. Vialard, M. Andres, H. Annamalai, S. Behera, N. D'Adamo, T. Doi, M. Feng, W. Han, N. Hardman-Mountford, H. Hendon, R. Hood, S. Kido, C. Lee, T. Lee, M. Lengaigne, J. Li, R. Lumpkin, K.N. Navaneeth, B. Milligan, M.J. Mcphaden, M. Ravichandran, T. Shinoda, A. Singh, B. Sloyan, P.G. Strutton, A.C. Subramanian, S. Thurston, T. Tozuka, C.C. Ummenhofer, A.S. Unnikrishnan, R. Venkatesan, D. Wang, J. Wiggert, L. Yu, W. Yu

Faculty Publications

The Indian Ocean is warming faster than any of the global oceans and its climate is uniquely driven by the presence of a landmass at low latitudes, which causes monsoonal winds and reversing currents. The food, water, and energy security in the Indian Ocean rim countries and islands are intrinsically tied to its climate, with marine environmental goods and services, as well as trade within the basin, underpinning their economies. Hence, there are a range of societal needs for Indian Ocean observation arising from the influence of regional phenomena and climate change on, for instance, marine ecosystems, monsoon rains, and …

Beyond Static Benchmarking: Using Experimental Manipulations To Evaluate Land Model Assumptions, William R. Wieder, David M. Lawrence, Rosie A. Fisher, Gordon B. Bonan, Susan J. Cheng, Christine L. Goodale, A. Stuart Grandy, Charles D. Koven, Danica L. Lombardozzi, Keith W. Oleson, R. Quinn Thomas

Faculty Publications

Land models are often used to simulate terrestrial responses to future environmental changes, but these models are not commonly evaluated with data from experimental manipulations. Results from experimental manipulations can identify and evaluate model assumptions that are consistent with appropriate ecosystem responses to future environmental change. We conducted simulations using three coupled carbon-nitrogen versions of the Community Land Model (CLM, versions 4, 4.5, and—the newly developed—5), and compared the simulated response to nitrogen (N) and atmospheric carbon dioxide (CO2) enrichment with meta-analyses of observations from similar experimental manipulations. In control simulations, successive versions of CLM showed a poleward increase in …

Feasibility Of Generating Synthetic Ct From T1-Weighted Mri Using A Linear Mixed-Effects Regression Model, Anant Pandey, S. A. Yoganathan, Beibei Guo, Rui Zhang

Faculty Publications

Generation of synthetic computed tomography (sCT) for magnetic resonance imaging (MRI)-only radiotherapy is emerging as a promising direction because it can eliminate the registration error and simplify clinical workflow. The goal of this study was to generate accurate sCT from standard T1-weighted MRI for brain patients. CT and MRI data of twelve patients with brain tumors were retrospectively collected. Linear mixed-effects regression models were fitted between CT and T1-weighted MRI intensities for different segments in the brain. The whole brain sCTs were generated by combining predicted segments together. Mean absolute error (MAE) between real CTs and sCTs across all patients …

The Cost Of Improving Nutritional Outcomes Through Food‐Assisted Maternal And Child Health And Nutrition Programmes In Burundi And Guatemala, Jessica Heckert, Jef L. Leroy, Deanna K. Olney, Susan Richter, Elyse Iruhiriye, Marie T. Ruel

Faculty Publications

Evidence on the cost‐effectiveness of multisectoral maternal and child health and nutrition programmes is scarce. We conducted a prospective costing study of two food‐assisted maternal and child health and nutrition programmes targeted to pregnant women and children during the first 1,000 days (pregnancy to 2 years). Each was paired with a cluster‐randomized controlled trial to evaluate impact and compare the optimal quantity and composition of food rations (Guatemala, five treatment arms) and their optimal timing and duration (Burundi, three treatment arms). We calculated the total and per beneficiary cost, conducted cost consequence analyses, and estimated the cost savings from extending …

Linking Nutrient Stoichiometry To Zika Virus Transmission In A Mosquito, Andrew S. Paige, Shawna K. Bellamy, Barry W. Alto, Catherine L. Dean, Donald A. Yee

Faculty Publications

Food quality and quantity serve as the basis for cycling of key chemical elements in trophic interactions; yet the role of nutrient stoichiometry in shaping host–pathogen interactions is under appreciated. Most of the emergent mosquito-borne viruses affecting human health are transmitted by mosquitoes that inhabit container systems during their immature stages, where allochthonous input of detritus serves as the basal nutrients. Quantity and type of detritus (animal and plant) were manipulated in microcosms containing newly hatched Aedes aegypti mosquito larvae. Adult mosquitoes derived from these microcosms were allowed to ingest Zika virus-infected blood and then tested for disseminated infection, transmission, …

Towards On-Demand E. Coli-Based Cell-Free Protein Synthesis Of Tissue Plasminogen Activator, Seung-Ook Yang, Gregory H. Nielsen, Kristen M. Wilding, Merideth A. Cooper, David W. Wood, Bradley Charles Bundy

Faculty Publications

Stroke is the leading cause of death with over 5 million deaths worldwide each year. About 80% of strokes are ischemic strokes caused by blood clots. Tissue plasminogen activator (tPa) is the only FDA-approved drug to treat ischemic stroke with a wholesale price over $6000. tPa is now off patent although no biosimilar has been developed. The production of tPa is complicated by the 17 disulfide bonds that exist in correctly folded tPA. Here, we present an Escherichia coli-based cell-free protein synthesis platform for tPa expression and report conditions which resulted in the production of active tPa. While the activity …

Discovery And Characterization Of Bacteriophage Luckybarnes, Savannah L. Underwood, Amanda Foto, Amanda F. Ray, Alexander E. Nelms, Keyshawn L. Kennedy, Shelby G. Hartley, Logan M. Ryals, Chandan Gurung, William A. D'Angelo, Welkin H. Pope, Dmitri V. Mavrodi

Faculty Publications

Here, we report the genome sequence of LuckyBarnes, a newly isolated singleton siphovirus that infects Brevibacterium iodinum ATCC 15728 and has a 50,774-bp genome with 67 predicted genes.

Populations Are Not Declining And Food Webs Are Not Collapsing At The Luquillo Experimental Forest, M. R. Willig, L. Woolbright, S. J. Presley, T. D. Schowalter, R. B. Waide, T. Heartsill Scalley, J. K. Zimmerman, G. González, A. E. Lugo

Faculty Publications

No abstract provided.

Managing With Low Milk Prices: Three Areas That Can Help Your Bottom Line, Peter S. Erickson

Faculty Publications

No abstract provided.

Repurposing Of Glycine-Rich Proteins In Abiotic And Biotic Stresses In The Lone-Star Tick (Amblyomma Americanum), Rebekah Bullard, Surendra Raj Sharma, Pradipta Kumar Das, Sarah E. Morgan, Shahid Karim

Faculty Publications

Tick feeding requires the secretion of a huge number of pharmacologically dynamic proteins and other molecules which are vital for the formation of the cement cone, the establishment of the blood pool and to counter against the host immune response. Glycine-rich proteins (GRP) are found in many organisms and can function in a variety of cellular processes and structures. The functional characterization of the GRPs in the tick salivary glands has not been elucidated. GRPs have been found to play a role in the formation of the cement cone; however, new evidence suggests repurposing of GRPs in the tick physiology. …

Changes In The Spatial Distribution And Anatomy Of A Range Shift For The Atlantic Surfclam Spisula Solidissima In The Mid-Atlantic Bight And On Georges Bank, Jeremy R. Timbs, Eric N. Powell, Roger Mann

Faculty Publications

The Atlantic surfclam Spisula solidissima supports one of the largest fisheries on the US northeast coast. Using ~30 yr of data from surfclam stock surveys, variance-to-mean ratios (VtMRs) were calculated both temporally and spatially for a range of surfclam size classes to determine the degree of patchiness. The VtMR declined from the 1980s to present in all regions (offshore Delmarva, New Jersey, Long Island, Southern New England, Georges Bank); however, VtMR rose with increasing clam size. Taylor’s power law (TPL) analysis corroborated the VtMR; the surfclam is highly patchy across its range. The surfclam’s proclivity for a patchy distribution varied …

Linking Water Quality To Aedes Aegypti And Zika In Flood-Prone Neighborhoods, Susan Harrell Yee, Donald A. Yee, Rebeca De Jesus Crespo, Autumn Oczkowski, Fengwei Bai, Stephanie Friedman

Faculty Publications

The ability of ecosystems to regulate water quality and flood events has been linked to health outcomes, including mosquito-borne illnesses. In the San Juan Bay Estuary watershed of Puerto Rico, habitat alterations and land-use development have disrupted watershed hydrology, exacerbating wastewater discharges and subjecting some neighborhoods to frequent flooding events. In 2016, the mosquito-borne illness Zika became a new cause for concern. We hypothesized that nutrient-enriched flood water could provide pulses of supplemental nutrients to local mosquito populations. We conducted a field study in six neighborhoods adjacent to the estuary to assess whether environmental variability of nutrient inputs could be …

Habitat Preference Modulates Transoceanic Dispersal In A Terrestrial Vertebrate, Mozes P.K. Blom, Nicholas J. Matzke, Jason G. Bragg, Evy Arida, Christopher C. Austin, Adam R. Backlin, Miguel A. Carretero, Robert N. Fisher, Frank Glaw, Stacie A. Hathaway, Djoko T. Iskandar, Jimmy A. Mcguire, Benjamin R. Karin, Sean B. Reilly, Eric N. Rittmeyer, Sara Rocha, Mickaël Sanchez, Alexander L. Stubbs, Miguel Vences, Craig Moritz

Faculty Publications

© 2019 The Author(s) Published by the Royal Society. All rights reserved. The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur …

The Longest-Lasting Relationship: Patterns Of Contact And Well-Being Among Mid- To Later-Life Siblings, Alexander C. Jensen, Makayla K. Nielson, Jeremy B. Yorgason

Faculty Publications

Objectives: Adults in mid to later life experience shrinking social networks, which may hinder well-being. Siblings may be important sources of social contact. Yet, little is known about adults’ patterns of contact with siblings and how contact is linked to well-being.

Method: Participants included 491 adults from across the United States (M age = 58.96, SD = 6.25; 68% female) recruited online via Amazon Mechanical Turk; they reported on their contact with their sibling in person, over the phone, via email, texting, and social media.

Results: Latent class analysis found evidence for four patterns of contact (classes) among siblings: low, …

Approaches For Sample Characterization And Lithography With Nanoparticles Using Modes Of Scanning Probe Microscopy, Jayne C. Garno, Temitope O. Jegede, Kathryn B. Mckee, Melissia Porter, Autumn E. Webb, Jin Gyun Lee, Neepa Mk Kuruppu Arachchige, Justin R. Ragains, Noémie Elgrishi

Faculty Publications

Measurement and imaging modes of scanning probe microscopy (SPM) have been routinely applied for characterizing systems of nanoparticles; however the evolution of fabrication methods to prepare arrangements of nanoparticles remains a challenge. Reproducible fabrication of surface structures which integrate nanoparticles within ultra-small patterns will require innovative approaches to achieve high throughput and precision. Strategies for nanoscale lithography have been introduced for preparing defined arrangements of nanoparticles on surfaces based on physical or chemical interactions. For example, physisorption was employed for attaching nanoparticles based on colloidal lithography and site-directed assembly. Microfabricated atomic force microscope (AFM) tips with capillary channels have been …

Preserving Mars Today Using Baseline Ecologies, Daniel S. Capper

Faculty Publications

Current calls to protect the Martian environment with “Planetary Parks” maintain environmental merit. However, they lack a sufficiently urgent timeframe for initiating protection as well as a robust scientific method for the establishment of noteworthy Martian natural landmarks as natural reserves. In response, if we return to the seminal environmental preservation teachings of Aldo Leopold and John Muir, we encounter the importance of grounding Martian preservation efforts on the fundamental environmental science method of a base-datum of normality, or baseline ecology. This method establishes natural reserves that feature both minimal human interference as well as known origination dates, thereby providing …

Is Selenoprotein K Required For Borrelia Burgdorferi Infection Within The Tick Vector Ixodes Scapularis?, Deepak Kumar, Monica Embers, Thomas N. Mather, Shahid Karim

Faculty Publications

Background: Tick selenoproteins are involved in regulating oxidative and endoplasmic reticulum stress during prolonged tick feeding on mammalian hosts. How selenoproteins are activated upon tick-borne pathogen infection is yet to be defined.

Methods: To examine the functional role of selenoprotein K in Borrelia burgdorferi infection within the tick host Ixodes scapularis, RNA interference (RNAi)-based gene silencing was performed.

Results: Selenoprotein K is an endoplasmic reticulum (ER)-resident protein and a component of the ERAD complex involved in ER homeostasis. A qRT-PCR assay revealed the significant upregulation of selenogene K (selenoK) expression in B. burgdorferi-infected …

Highlights From The American Heart Association's Epi|Lifestyle 2019 Scientific Sessions, Alvaro Alonso, Madison D. Anderson, Michael P. Bancks, Sherry Ann Brown, Melissa C. Caughey, Alex R. Chang, Erin Delker, Kathryn Foti, Véronique Gingras, Michael G. Nanna, Alexander C. Razavi, Jewel Scott Phd, Rn, Fnp-C, Elizabeth Selvin, Catherine Tcheandjieu, Alvin G. Thomas, Ruth Alma N. Turkson-Ocran, Allison Webel, Deborah R. Young, Bailey M. Debarmore

Faculty Publications

No abstract provided.

Highlights From The American Heart Association's Epi|Lifestyle 2019 Scientific Sessions, Alvaro Alonso, Madison D. Anderson, Michael P. Bancks, Sherry Ann Brown, Melissa C. Caughey, Alex R. Chang, Erin Delker, Kathryn Foti, Véronique Gingras, Michael G. Nanna, Alexander C. Razavi, Jewel Scott Phd, Rn, Fnp-C, Elizabeth Selvin, Catherine Tcheandjieu, Alvin G. Thomas, Ruth Alma N. Turkson-Ocran, Allison Webel, Deborah R. Young, Bailey M. Debarmore

Faculty Publications

No abstract provided.

"You Can't Go Back To Holding Hands." Reading Judy Blume's Forever In The #Metoo Era, Jenna Spiering, Kate Kedley

Faculty Publications

Judy Blume’s Forever is a cultural artifact that gives readers a historical look at society’s attitudes about sex and sexuality at the time of publication in 1975. However, in the #MeToo era, Blume’s text is poised for new analysis in light of important conversations and concerns about sex, sexuality, and consent. In this article, Critical Youth Studies and Queer Theory are used to explore the ways in which young readers can critically engage with Blume’s novel and questions about virginity, sex, sexuality, and consent associated with the #MeToo movement.